14-82911659-T-G

Variant names:

• chr14-82911659-T-G
• rs12050412

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.196 in 152,100 control chromosomes in the GnomAD database, including 3,055 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29869 AN: 151982 Hom.: 3051 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29885 AN: 152100 Hom.: 3055 Cov.: 32 AF XY: 0.198 AC XY: 14715 AN XY: 74342

African (AFR) AF: 0.179 AC: 7420 AN: 41536

American (AMR) AF: 0.221 AC: 3377 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1042 AN: 5164

South Asian (SAS) AF: 0.155 AC: 745 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2323 AN: 10574

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13583 AN: 67960

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.198 Hom.: 8045

Bravo AF: 0.195

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12050412; hg19: chr14-83378003;